Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_011912148.1 PST_RS04900 glutamate 5-kinase
Query= SwissProt::O04226 (716 letters) >NCBI__GCF_000013785.1:WP_011912148.1 Length = 372 Score = 140 bits (352), Expect = 1e-37 Identities = 89/280 (31%), Positives = 147/280 (52%), Gaps = 19/280 (6%) Query: 8 RSFVRDVKRVIIKVGTAVVSRQDGRLALGRVGALCEQVKELNSLGYEVILVTSGAVGVGR 67 R V +R ++K+G+A+++ L + +Q+ L + G E++LV+SGAV G Sbjct: 2 RDKVSGARRWVVKIGSALLTADGRGLDQAAMAVWVDQMVALRAAGVELVLVSSGAVAAGM 61 Query: 68 QRLRYRKLVNSSFADLQKPQMELDGKACAAVGQSGLMALYDMLFNQLDVSSSQLLVTDSD 127 RL + +P+ + +A AAVGQ GL+ ++ F + D ++Q+LVT D Sbjct: 62 SRLGWAS----------RPKAVHELQAAAAVGQMGLIRAWESSFARCDQQTAQILVTHDD 111 Query: 128 FENPKFREQLTETVESLLDLKVIPIFNENDAISTRKAPYEDSSGIFWDNDSLAGLLALEL 187 + K T+ +L+DL V+P+ NEND + T + F DND+LA L+A + Sbjct: 112 LSDRKRYLNARSTLRTLIDLGVVPVINENDTVVTDEIR-------FGDNDTLAALVANLV 164 Query: 188 KADLLILLSDVDGLYSGPP-SEPSSKII-HTYIKEKHQQEITFGDKSRVGRGGMTAKVKA 245 +ADLL++L+D DG++ P P + +I + + G +GRGGM K++A Sbjct: 165 EADLLVILTDRDGMFDADPRHNPEANLISEARADDPALDAVAGGTGGALGRGGMQTKLRA 224 Query: 246 AVLASNSGTPVVITSGFENRSILKVLHGEKIGTLFHKNAN 285 A LA+ SG VI G + + ++ GE++GTL N Sbjct: 225 ARLAARSGAHTVIVGGRIEQVLSRLKAGERLGTLLAPECN 264 Lambda K H 0.317 0.134 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 512 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 716 Length of database: 372 Length adjustment: 35 Effective length of query: 681 Effective length of database: 337 Effective search space: 229497 Effective search space used: 229497 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory